Skip to contents

Convert between tbl_now and EpiNow2

tbl_now_EpiNow2.Rd

[Experimental]

EpiNow2 takes four different input shapes, one per entry point, so tbl_now_to_EpiNow2() is told which one you want with target – named after the EpiNow2 function the result is passed to, so it can be handed over unchanged:

"estimate_infections"

a data.frame of date / confirm, the series as known at get_now(). Also what EpiNow2::epinow() takes.

"regional_epinow"

the same, plus a region column built from the object's strata.

"estimate_truncation"

a tbl_now_epinow2_snapshots list – one date/confirm snapshot per report date, which is the one EpiNow2 model that uses the report dimension a tbl_now exists to carry.

"estimate_dist"

the interval-censored pdate_lwr / pdate_upr / sdate_lwr / sdate_upr / obs_date frame that EpiNow2::estimate_dist() fits a delay distribution to (new in EpiNow2 1.9.0). Count data rides along as the n weight column.

tbl_now_from_EpiNow2() inverts the snapshot form: snapshot k is the series as known at report date k, so differencing consecutive snapshots recovers count-incidence exactly. There is deliberately no inverse for the other three: a single series has no report dimension to recover, and a delay distribution is not case data.

Usage

tbl_now_to_EpiNow2(
  x,
  ...,
  target = c("estimate_infections", "regional_epinow", "estimate_truncation",
    "estimate_dist"),
  snapshots = NULL,
  accumulate = "auto",
  verbose = TRUE,
  quiet = FALSE
)

tbl_now_from_EpiNow2(data, ..., report_dates = NULL, verbose = TRUE)

Arguments

x

A tbl_now object.

...

Forwarded to as_tbl_now() (from); unused (to).

target

Which EpiNow2 entry point the result is for. See above.

snapshots

For "estimate_truncation": how many snapshots to emit, taken from the latest report dates. NULL (default) uses 5, matching EpiNow2::example_truncated. One snapshot per distinct report date is usually far more than the model can fit.

accumulate

How to handle non-daily data. "auto" (default) lays a weekly series on EpiNow2's daily grid with an accumulate column; FALSE passes the rows through unchanged, which is almost always wrong (see Non-daily data). Ignored for "estimate_dist", which works in censoring windows rather than on a grid.

verbose

Logical. Print the choices that were made.

quiet

Logical. A different channel from verbose: verbose controls the informational summary of what the conversion did, while quiet suppresses the lossy-conversion warning. Set both to keep a conversion entirely silent.

data

A tbl_now_epinow2_snapshots, or a plain list of date/confirm data frames (e.g. EpiNow2::example_truncated), in which case report_dates is required.

report_dates

For from: a Date vector, one per snapshot, saying when each was taken. Read from the object's attribute when it has one.

Value

For to, a data.frame or a tbl_now_epinow2_snapshots, according to target. For from, a tbl_now of data_type = "count-incidence".

Non-daily data

EpiNow2 models a daily process. As of 1.9.0 there is no timestep, interval or period argument on any of its entry points, so a weekly series passed as one row per week is read as one row per day and the fit is silently wrong on the time axis – no error, just an epidemic seven times too fast.

Its own answer is the accumulate column (see EpiNow2::fill_missing()): the series is laid on a daily grid and the filler days are marked to be added to the next real observation. accumulate = "auto" does this from get_event_units(). Units coarser than a week, and the "numeric" grid, are refused outright rather than approximated.

What EpiNow2 will not take

  • EpiNow2::estimate_secondary() models two data streams (cases and deaths, say) against each other. One tbl_now is one stream, so there is no honest mapping and no target for it.

  • EpiNow2::estimate_delay() takes a bare vector of delays. Its own help now points at estimate_dist() as "the recommended replacement", and it throws away the censoring a tbl_now carries, so there is no target for it either. If you want it anyway, it is x$.delay.

See also

tbl_now_to_epidist(), which builds the same censoring windows as target = "estimate_dist" – the two are different front ends onto one delay-distribution schema.

Examples

data(denguedat)
nowobj <- tbl_now(denguedat[1:2000, ],
  event_date = "onset_week", report_date = "report_week", verbose = FALSE
)
## A single daily series for estimate_infections() -- the weekly data is laid
# on EpiNow2's daily grid.
head(tbl_now_to_EpiNow2(nowobj, verbose = FALSE, quiet = TRUE))
#>         date confirm accumulate
#> 1 1989-12-26      NA       TRUE
#> 2 1989-12-27      NA       TRUE
#> 3 1989-12-28      NA       TRUE
#> 4 1989-12-29      NA       TRUE
#> 5 1989-12-30      NA       TRUE
#> 6 1989-12-31      NA       TRUE

## Snapshots for estimate_truncation(), which uses the report dimension.
snaps <- tbl_now_to_EpiNow2(nowobj,
  target = "estimate_truncation", verbose = FALSE, quiet = TRUE
)
snaps
#> ── 5 reporting snapshots from a <tbl_now> ──────────────────────────────────────
#> • One per report date: "1991-01-21", "1991-01-28", "1991-02-11", "1991-02-25", and "1991-03-04"
#> • Rows each: 357, 357, 357, 357, and 357
#> • Now: "1991-03-04"
#> ℹ Pass this to `EpiNow2::estimate_truncation()`. `EpiNow2::estimate_secondary()` wants a single data frame of linked series instead -- not this.